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I had a similar issue (although the delta was much smaller). Eventually, I had to remove the local DB on my Windows and Mac clients. (Or you could try the standard uninstall / re-install). Before doing so, I reviewed what I had in the "Conflicting Changes" folder on my clients to make sure there wasn't a note missing from online Evernote since as @DTLow mentions that it is your master copy.

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This has happened to me a while back. I think it was the result of an incomplete sync, or some event that interrupted EN.

I was able to find the notes starting by comparing counts by notebook, arduous for me since I don't have many notebooks. Had to do searches by date range within notebook starting most recent. When I found a delta by date range I would add a temp tag on my PC to that date range, sync, and then find the notes on the Web without the temp tag. Then add the temp tag to those notes, sync and the notes would appear on my PC. PITA, but it worked.

I didn't just download since I felt if something wasn't coming down it might not be going up, turned out to be the case. But this was way back, it hasn't happened to me in a long time.

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Given that the web count is 127 notes less than my two independent desktop counts (macOS and Win10) suggests that I should NOT force a new download from the server. Unless the web app is not displaying the correct count from the database I have no idea how to start to reconcile these discrepancies and figure out which notes are missing from which client platform.

I hope that this is not an issue with Evernote Business accounts. I can imagine the negative reaction from corporate users if they were to notice a discrepancy in note counts. One response would be to immediately forbid the use of Evernote to store business-critical data.

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Do you have offline notebooks on your iPad/iPhone; otherwise the mobile platforms retrieve data from the server

No offline notebooks. What concerns me is that both iOS devices and the web app show different counts. How do I identify the notes at appear not to be syncing to the mobile devices? And the notes that are not visible via the web app?

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Is it possible that there are duplicated notes in the desktop databases? I have to admit that it's odd that they have an identical number that is different from the Web note count. Another possibility is local notebooks on the desktops. I just checked and found that my desktop count was 1 higher than my Web count, and it was due to a local notebook with 1 note in it. But those large discrepancies are kind of disturbing.

EDIT: The way I tracked down the source of my 1-note discrepancy was to methodically go down my list of notebooks in the desktop (Windows) program, with the Web version open side-by-side. It would be really tedious to do that with over 5,000 notes, @sdolan, but at least it's easy to compare the totals for each notebook and discover whether the discrepancies are spread throughout the notebooks or limited to just certain ones.

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No offline notebooks. What concerns me is that both iOS devices and the web app show different counts. How do I identify the notes at appear not to be syncing to the mobile devices? And the notes that are not visible via the web app?

Do a the same created date range search on all devices, compare the counts.

If they are different add a temp tag to all the notes on your Mac or PC and sync (easier to make mass changes there).

If the extra notes are on your Mac/PC this should force the notes to the other devices.

If the extra notes are on the iDevices do a -tag:temp with the date search there. Tag the remaining notes with temp and sync. This should force the notes to the other devices.

When the totals match for the date range, delete the temp tag and continue the date ranges till done.